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- PDB-8ro2: Integrative Structure of the human intron lariat Spliceosome (ILS'') -

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Entry
Database: PDB / ID: 8ro2
TitleIntegrative Structure of the human intron lariat Spliceosome (ILS'')
Components
  • (CWF19-like protein ...) x 2
  • (Pre-mRNA-processing factor ...) x 2
  • (Pre-mRNA-splicing factor ...) x 5
  • (Small nuclear ribonucleoprotein ...) x 6
  • 116 kDa U5 small nuclear ribonucleoprotein component
  • ATP-dependent RNA helicase DHX15
  • Cell division cycle 5-like protein
  • Coiled-coil domain-containing protein 12
  • Crooked neck-like protein 1
  • INTRON
  • Intron-binding protein aquarius
  • PAX3- and PAX7-binding protein 1
  • Peptidyl-prolyl cis-trans isomerase-like 1
  • Pleiotropic regulator 1
  • Pre-mRNA-processing-splicing factor 8
  • Protein BUD31 homolog
  • SNW domain-containing protein 1
  • Small nuclear ribonucleoprotein-associated proteins B and B'
  • Spliceosome-associated protein CWC15 homolog
  • Splicing factor ESS-2 homolog
  • Splicing regulator SDE2
  • Tuftelin-interacting protein 11
  • U2 snRNA
  • U5 small nuclear ribonucleoprotein 40 kDa protein
  • U5 snRNA
  • U6 snRNA
KeywordsSPLICING / mRNA / intron lariat spliceosome / pre-mRNA
Function / homology
Function and homology information


RNA lariat debranching enzyme activator activity / spliceosomal complex disassembly / post-spliceosomal complex / biomineral tissue development / U2-type post-mRNA release spliceosomal complex / negative regulation of double-strand break repair via nonhomologous end joining / protection from non-homologous end joining at telomere / regulation of skeletal muscle satellite cell proliferation / regulation of retinoic acid receptor signaling pathway / post-mRNA release spliceosomal complex ...RNA lariat debranching enzyme activator activity / spliceosomal complex disassembly / post-spliceosomal complex / biomineral tissue development / U2-type post-mRNA release spliceosomal complex / negative regulation of double-strand break repair via nonhomologous end joining / protection from non-homologous end joining at telomere / regulation of skeletal muscle satellite cell proliferation / regulation of retinoic acid receptor signaling pathway / post-mRNA release spliceosomal complex / U2 snRNP binding / U7 snRNA binding / histone pre-mRNA DCP binding / 3'-5' RNA helicase activity / endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / U7 snRNP / generation of catalytic spliceosome for first transesterification step / positive regulation of myoblast proliferation / histone methyltransferase binding / histone pre-mRNA 3'end processing complex / regulation of vitamin D receptor signaling pathway / SLBP independent Processing of Histone Pre-mRNAs / SLBP Dependent Processing of Replication-Dependent Histone Pre-mRNAs / nuclear retinoic acid receptor binding / embryonic brain development / protein methylation / oocyte development / response to alkaloid / U12-type spliceosomal complex / alternative mRNA splicing, via spliceosome / 7-methylguanosine cap hypermethylation / U1 snRNP binding / sno(s)RNA-containing ribonucleoprotein complex / methylosome / mRNA 3'-end processing / RNA splicing, via transesterification reactions / ATP-dependent activity, acting on RNA / pICln-Sm protein complex / U2-type catalytic step 1 spliceosome / pre-mRNA binding / snRNP binding / positive regulation of mRNA splicing, via spliceosome / small nuclear ribonucleoprotein complex / SMN-Sm protein complex / spliceosomal tri-snRNP complex / host-mediated activation of viral transcription / P granule / telomerase holoenzyme complex / U2-type precatalytic spliceosome / positive regulation of vitamin D receptor signaling pathway / commitment complex / telomerase RNA binding / mRNA cis splicing, via spliceosome / U2-type spliceosomal complex / nuclear vitamin D receptor binding / U2-type prespliceosome assembly / Notch binding / Transport of Mature mRNA derived from an Intron-Containing Transcript / Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells / U2-type catalytic step 2 spliceosome / RUNX3 regulates NOTCH signaling / positive regulation of neurogenesis / NOTCH4 Intracellular Domain Regulates Transcription / U4 snRNP / RNA Polymerase II Transcription Termination / U2 snRNP / U1 snRNP / NOTCH3 Intracellular Domain Regulates Transcription / U2-type prespliceosome / inner cell mass cell proliferation / protein peptidyl-prolyl isomerization / WD40-repeat domain binding / ubiquitin-ubiquitin ligase activity / K63-linked polyubiquitin modification-dependent protein binding / nuclear androgen receptor binding / snoRNA binding / precatalytic spliceosome / muscle organ development / generation of catalytic spliceosome for second transesterification step / Notch-HLH transcription pathway / lipid biosynthetic process / Formation of paraxial mesoderm / positive regulation of transforming growth factor beta receptor signaling pathway / SMAD binding / spliceosomal complex assembly / mitotic G2 DNA damage checkpoint signaling / mRNA Splicing - Minor Pathway / mRNA 3'-splice site recognition / spliceosomal tri-snRNP complex assembly / Prp19 complex / blastocyst development / U5 snRNA binding / protein K63-linked ubiquitination / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / U5 snRNP / protein localization to nucleus / positive regulation of G1/S transition of mitotic cell cycle / embryonic organ development / U2 snRNA binding / U6 snRNA binding
Similarity search - Function
Intron Large complex component GCFC2-like / Septin and tuftelin interacting protein / Nuclear protein DGCR14/ESS-2 / Tuftelin interacting protein, N-terminal domain / : / Nuclear protein Es2 / Tuftelin interacting protein N terminal / Vertebrate Splicing regulator sde2, N-terminal ubiquitin domain / GCF, C-terminal / GC-rich sequence DNA-binding factor-like protein ...Intron Large complex component GCFC2-like / Septin and tuftelin interacting protein / Nuclear protein DGCR14/ESS-2 / Tuftelin interacting protein, N-terminal domain / : / Nuclear protein Es2 / Tuftelin interacting protein N terminal / Vertebrate Splicing regulator sde2, N-terminal ubiquitin domain / GCF, C-terminal / GC-rich sequence DNA-binding factor-like protein / mRNA splicing factor Cwf18-like / TFP11/STIP/Ntr1 / : / cwf18 pre-mRNA splicing factor / Splicing regulator SDE2, SDE2 domain / Cwf19-like protein, C-terminal domain-2 / Cwf19-like, C-terminal domain-1 / Cwf19-like protein / Protein similar to CwfJ C-terminus 2 / Protein similar to CwfJ C-terminus 1 / DHX15, DEXH-box helicase domain / Pre-mRNA-splicing factor Isy1 / Pre-mRNA-splicing factor Isy1 superfamily / Isy1-like splicing family / Prp19 WD40 domain / : / : / Intron-binding protein aquarius, beta-barrel / Intron-binding protein aquarius insert domain / Pre-mRNA-splicing factor SPF27 / Breast carcinoma amplified sequence 2 (BCAS2) / CWF11 family / Intron-binding protein aquarius, N-terminal / Intron-binding protein aquarius N-terminal / mRNA splicing factor SYF2 / SYF2 splicing factor / Helix hairpin bin domain superfamily / : / Replication stress response SDE2 C-terminal / G-patch domain / G-patch domain profile. / G-patch domain / glycine rich nucleic binding domain / Pre-mRNA-processing factor 17 / : / Pre-mRNA-splicing factor 19 / Pre-mRNA-processing factor 19 / : / Prp19/Pso4-like / : / Pre-mRNA-splicing factor SYF1 middle HAT repeat / G10 protein signature 2. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase, cyclophilin A-like / U-box domain / BUD31/G10-related, conserved site / G10 protein signature 1. / : / STL11, N-terminal / : / Pre-mRNA-splicing factor Syf1/CRNKL1 C-terminal HAT repeat / DNA2/NAM7 helicase, helicase domain / AAA domain / SKI-interacting protein SKIP, SNW domain / SKI-interacting protein, SKIP / SKIP/SNW domain / : / Pre-mRNA-splicing factor Syf1/CNRKL1 N-terminal HAT repeat / Pre-mRNA-splicing factor Cwf15/Cwc15 / Cwf15/Cwc15 cell cycle control protein / WD repeat Prp46/PLRG1-like / Pre-mRNA-splicing factor Cwc2/Slt11 / : / G10 protein / Pre-mRNA-splicing factor BUD31 / Pre-mRNA splicing factor component Cdc5p/Cef1, C-terminal / : / : / pre-mRNA splicing factor component / DNA2/NAM7-like helicase / : / Small ribonucleoprotein associated, SmB/SmN / Myb-like DNA-binding domain / Small nuclear ribonucleoprotein D1 / U-box domain profile. / HIT-like superfamily / Zinc finger, CCCH-type superfamily / Modified RING finger domain / U-box domain / zinc finger / 116kDa U5 small nuclear ribonucleoprotein component, N-terminal / 116kDa U5 small nuclear ribonucleoprotein component, C-terminal / Snu114, GTP-binding domain / 116 kDa U5 small nuclear ribonucleoprotein component N-terminus / Pre-mRNA-splicing factor Syf1-like / : / Helicase associated domain (HA2), ratchet-like / DEAD-box helicase, OB fold / Oligonucleotide/oligosaccharide-binding (OB)-fold / Helicase associated domain (HA2), winged-helix / Helicase-associated domain
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / INOSITOL HEXAKISPHOSPHATE / : / : / : / RNA / RNA (> 10) / RNA (> 100) / ATP-dependent RNA helicase DHX15 / Pleiotropic regulator 1 ...GUANOSINE-5'-TRIPHOSPHATE / INOSITOL HEXAKISPHOSPHATE / : / : / : / RNA / RNA (> 10) / RNA (> 100) / ATP-dependent RNA helicase DHX15 / Pleiotropic regulator 1 / RNA helicase aquarius / Pre-mRNA-processing factor 17 / Pre-mRNA-splicing factor SPF27 / Pre-mRNA-splicing factor SYF2 / Small nuclear ribonucleoprotein-associated proteins B and B' / Protein BUD31 homolog / Small nuclear ribonucleoprotein E / Small nuclear ribonucleoprotein F / Small nuclear ribonucleoprotein G / Small nuclear ribonucleoprotein Sm D1 / Small nuclear ribonucleoprotein Sm D2 / Small nuclear ribonucleoprotein Sm D3 / SNW domain-containing protein 1 / 116 kDa U5 small nuclear ribonucleoprotein component / CWF19-like protein 2 / CWF19-like protein 1 / Splicing regulator SDE2 / Pre-mRNA-processing-splicing factor 8 / Coiled-coil domain-containing protein 12 / Splicing factor ESS-2 homolog / U5 small nuclear ribonucleoprotein 40 kDa protein / Cell division cycle 5-like protein / Crooked neck-like protein 1 / Pre-mRNA-splicing factor SYF1 / Pre-mRNA-splicing factor RBM22 / Spliceosome-associated protein CWC15 homolog / Tuftelin-interacting protein 11 / Pre-mRNA-splicing factor ISY1 homolog / Pre-mRNA-processing factor 19 / Peptidyl-prolyl cis-trans isomerase-like 1 / PAX3- and PAX7-binding protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsRothe, P. / Vorlaender, M.K. / Plaschka, C.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Research Council (ERC)European Union
CitationJournal: Nature / Year: 2024
Title: Mechanism for the initiation of spliceosome disassembly.
Authors: Matthias K Vorländer / Patricia Rothe / Justus Kleifeld / Eric D Cormack / Lalitha Veleti / Daria Riabov-Bassat / Laura Fin / Alex W Phillips / Luisa Cochella / Clemens Plaschka /
Abstract: Precursor-mRNA (pre-mRNA) splicing requires the assembly, remodelling and disassembly of the multi-megadalton ribonucleoprotein complex called the spliceosome. Recent studies have shed light on ...Precursor-mRNA (pre-mRNA) splicing requires the assembly, remodelling and disassembly of the multi-megadalton ribonucleoprotein complex called the spliceosome. Recent studies have shed light on spliceosome assembly and remodelling for catalysis, but the mechanism of disassembly remains unclear. Here we report cryo-electron microscopy structures of nematode and human terminal intron lariat spliceosomes along with biochemical and genetic data. Our results uncover how four disassembly factors and the conserved RNA helicase DHX15 initiate spliceosome disassembly. The disassembly factors probe large inner and outer spliceosome surfaces to detect the release of ligated mRNA. Two of these factors, TFIP11 and C19L1, and three general spliceosome subunits, SYF1, SYF2 and SDE2, then dock and activate DHX15 on the catalytic U6 snRNA to initiate disassembly. U6 therefore controls both the start and end of pre-mRNA splicing. Taken together, our results explain the molecular basis of the initiation of canonical spliceosome disassembly and provide a framework to understand general spliceosomal RNA helicase control and the discard of aberrant spliceosomes.
History
DepositionJan 11, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 18, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Data collection / Structure summary
Category: em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
2: U2 snRNA
6: U6 snRNA
C: 116 kDa U5 small nuclear ribonucleoprotein component
D: Pre-mRNA-splicing factor ISY1 homolog
DX: ATP-dependent RNA helicase DHX15
E: U5 small nuclear ribonucleoprotein 40 kDa protein
J: Crooked neck-like protein 1
K: Pre-mRNA-splicing factor SPF27
L1: CWF19-like protein 1
N: Protein BUD31 homolog
O: Pre-mRNA-splicing factor RBM22
Q: Intron-binding protein aquarius
R: SNW domain-containing protein 1
S: Peptidyl-prolyl cis-trans isomerase-like 1
W: Pre-mRNA-processing factor 17
Z: Coiled-coil domain-containing protein 12
a: Small nuclear ribonucleoprotein Sm D3
c: Small nuclear ribonucleoprotein Sm D1
d: Small nuclear ribonucleoprotein Sm D2
e: Small nuclear ribonucleoprotein E
f: Small nuclear ribonucleoprotein F
g: Small nuclear ribonucleoprotein G
s: Pre-mRNA-processing factor 19
z: Splicing regulator SDE2
3: Splicing factor ESS-2 homolog
5: U5 snRNA
A: Pre-mRNA-processing-splicing factor 8
I: Pre-mRNA-splicing factor SYF1
IN: INTRON
L: Cell division cycle 5-like protein
L2: CWF19-like protein 2
M: Pre-mRNA-splicing factor SYF2
P: Spliceosome-associated protein CWC15 homolog
PX: PAX3- and PAX7-binding protein 1
T: Pleiotropic regulator 1
TF: Tuftelin-interacting protein 11
b: Small nuclear ribonucleoprotein-associated proteins B and B'
q: Pre-mRNA-processing factor 19
r: Pre-mRNA-processing factor 19
t: Pre-mRNA-processing factor 19
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,326,67545
Polymers2,325,29540
Non-polymers1,3795
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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RNA chain , 4 types, 4 molecules 265IN

#1: RNA chain U2 snRNA


Mass: 60186.445 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: GenBank: 36516
#2: RNA chain U6 snRNA


Mass: 34098.270 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: GenBank: NR_004394.1
#26: RNA chain U5 snRNA


Mass: 36908.668 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: GenBank: 36515
#29: RNA chain INTRON


Mass: 30153.607 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)

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Protein , 18 types, 18 molecules CDXEJNQRSZz3ALPPXTTFb

#3: Protein 116 kDa U5 small nuclear ribonucleoprotein component / Elongation factor Tu GTP-binding domain-containing protein 2 / SNU114 homolog / hSNU114 / U5 snRNP- ...Elongation factor Tu GTP-binding domain-containing protein 2 / SNU114 homolog / hSNU114 / U5 snRNP-specific protein / 116 kDa / U5-116 kDa


Mass: 109560.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q15029
#5: Protein ATP-dependent RNA helicase DHX15 / ATP-dependent RNA helicase #46 / DEAH box protein 15 / Splicing factor Prp43 / hPrp43


Mass: 91065.805 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O43143, RNA helicase
#6: Protein U5 small nuclear ribonucleoprotein 40 kDa protein / U5-40K / 38 kDa-splicing factor / Prp8-binding protein / hPRP8BP / U5 snRNP-specific 40 kDa protein ...U5-40K / 38 kDa-splicing factor / Prp8-binding protein / hPRP8BP / U5 snRNP-specific 40 kDa protein / WD repeat-containing protein 57


Mass: 39359.492 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q96DI7
#7: Protein Crooked neck-like protein 1 / Crooked neck homolog / hCrn


Mass: 100610.008 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BZJ0
#10: Protein Protein BUD31 homolog / Protein EDG-2 / Protein G10 homolog


Mass: 17032.850 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P41223
#12: Protein Intron-binding protein aquarius / Intron-binding protein of 160 kDa / IBP160


Mass: 171502.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O60306, RNA helicase
#13: Protein SNW domain-containing protein 1 / Nuclear protein SkiP / Nuclear receptor coactivator NCoA-62 / Ski-interacting protein


Mass: 61770.648 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q13573
#14: Protein Peptidyl-prolyl cis-trans isomerase-like 1 / PPIase / Rotamase PPIL1


Mass: 18257.805 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9Y3C6, peptidylprolyl isomerase
#16: Protein Coiled-coil domain-containing protein 12


Mass: 19223.850 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q8WUD4
#24: Protein Splicing regulator SDE2 / Replication stress response regulator SDE2


Mass: 49818.027 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q6IQ49
#25: Protein Splicing factor ESS-2 homolog / DiGeorge syndrome critical region 13 / DiGeorge syndrome critical region 14 / DiGeorge syndrome ...DiGeorge syndrome critical region 13 / DiGeorge syndrome critical region 14 / DiGeorge syndrome protein H / DGS-H / Protein ES2


Mass: 52639.953 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q96DF8
#27: Protein Pre-mRNA-processing-splicing factor 8 / 220 kDa U5 snRNP-specific protein / PRP8 homolog / Splicing factor Prp8 / p220


Mass: 273974.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q6P2Q9
#30: Protein Cell division cycle 5-like protein / Cdc5-like protein / Pombe cdc5-related protein


Mass: 92406.883 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q99459
#33: Protein Spliceosome-associated protein CWC15 homolog


Mass: 26674.447 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9P013
#34: Protein PAX3- and PAX7-binding protein 1 / GC-rich sequence DNA-binding factor 1


Mass: 104953.656 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9Y5B6
#35: Protein Pleiotropic regulator 1


Mass: 57280.758 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O43660
#36: Protein Tuftelin-interacting protein 11 / Septin and tuftelin-interacting protein 1 / STIP-1


Mass: 96945.727 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9UBB9
#37: Protein Small nuclear ribonucleoprotein-associated proteins B and B' / snRNP-B / Sm protein B/B' / SmB/B'


Mass: 24642.131 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P14678

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Pre-mRNA-splicing factor ... , 5 types, 5 molecules DKOIM

#4: Protein Pre-mRNA-splicing factor ISY1 homolog


Mass: 33046.254 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9ULR0
#8: Protein Pre-mRNA-splicing factor SPF27 / Breast carcinoma-amplified sequence 2 / DNA amplified in mammary carcinoma 1 protein / Spliceosome- ...Breast carcinoma-amplified sequence 2 / DNA amplified in mammary carcinoma 1 protein / Spliceosome-associated protein SPF 27


Mass: 26163.420 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O75934
#11: Protein Pre-mRNA-splicing factor RBM22 / RNA-binding motif protein 22 / Zinc finger CCCH domain-containing protein 16


Mass: 46959.555 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9NW64
#28: Protein Pre-mRNA-splicing factor SYF1 / Protein HCNP / XPA-binding protein 2


Mass: 100148.711 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9HCS7
#32: Protein Pre-mRNA-splicing factor SYF2 / CCNDBP1-interactor / p29


Mass: 28780.518 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O95926

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CWF19-like protein ... , 2 types, 2 molecules L1L2

#9: Protein CWF19-like protein 1 / C19L1


Mass: 60696.922 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q69YN2
#31: Protein CWF19-like protein 2


Mass: 103976.492 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q2TBE0

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Pre-mRNA-processing factor ... , 2 types, 5 molecules Wsqrt

#15: Protein Pre-mRNA-processing factor 17 / Cell division cycle 40 homolog / EH-binding protein 3 / Ehb3 / PRP17 homolog / hPRP17


Mass: 65612.180 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O60508
#23: Protein
Pre-mRNA-processing factor 19 / Nuclear matrix protein 200 / PRP19/PSO4 homolog / hPso4 / RING-type E3 ubiquitin transferase PRP19 ...Nuclear matrix protein 200 / PRP19/PSO4 homolog / hPso4 / RING-type E3 ubiquitin transferase PRP19 / Senescence evasion factor


Mass: 55245.547 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
References: UniProt: Q9UMS4, RING-type E3 ubiquitin transferase

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Small nuclear ribonucleoprotein ... , 6 types, 6 molecules acdefg

#17: Protein Small nuclear ribonucleoprotein Sm D3 / Sm-D3 / snRNP core protein D3


Mass: 13940.308 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62318
#18: Protein Small nuclear ribonucleoprotein Sm D1 / Sm-D1 / Sm-D autoantigen / snRNP core protein D1


Mass: 13310.653 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62314
#19: Protein Small nuclear ribonucleoprotein Sm D2 / Sm-D2 / snRNP core protein D2


Mass: 13551.928 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62316
#20: Protein Small nuclear ribonucleoprotein E / snRNP-E / Sm protein E / SmE


Mass: 10817.601 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62304
#21: Protein Small nuclear ribonucleoprotein F / snRNP-F / Sm protein F / SmF


Mass: 9734.171 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62306
#22: Protein Small nuclear ribonucleoprotein G / snRNP-G / Sm protein G / SmG


Mass: 8508.084 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62308

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Non-polymers , 3 types, 5 molecules

#38: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#39: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#40: Chemical ChemComp-IHP / INOSITOL HEXAKISPHOSPHATE / MYO-INOSITOL HEXAKISPHOSPHATE / INOSITOL 1,2,3,4,5,6-HEXAKISPHOSPHATE


Mass: 660.035 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H18O24P6

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Details

Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Human Intron-lariat splicoesome / Type: COMPLEX
Entity ID: #1, #25-#26, #2, #27, #3-#6, #28-#29, #7-#8, #30, #9, #31-#32, #10-#11, #33-#34, #12-#14, #35-#36, #15-#17, #37, #18-#24
Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Buffer solutionpH: 7.9
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 750 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 87951 / Symmetry type: POINT

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